!scdrs perform-downstream\--h5ad-file single_cell_data/zeisel_2015/expr.h5ad\--score-file single_cell_data/cwy/{trait}.full_score.gz\--out-folder single_cell_data/cwy/\--group-analysis level1class\--flag-filter-data True\--flag-raw-count True SCZ在不同细胞的表达水平差异: # scDRS ...
The term post-GWAS analyses here refers to two somewhat distinct general topics; first are a compendium of analyses that are typically performed after one or more GWAS studies of a particular disease have been completed. These analyses include pooled or meta-analysis used in order to combine ...
第一、鉴定表型相关的细胞类型,比如下图: image 第二、发现疾病的subpopulations: image 3、scDRS安装与运行 3.1 下载、安装 #下载安装jupyter pip3 install jupyter #下载安装scDRS git clone https://github.com/martinjzhang/scDRS.git cd scDRS git checkout -b v102 v1.0.2 pip install -e . 3.2 ...
Post-GWAS analysis of six substance use traits improves the identification and functional interpretation of genetic risk lociBackground: Little is known about the functional mechanisms through which genetic loci associated with substance use traits ascertain their effect. This study aims to identify and ...
eQTL、mQTL共定位分析属于Post-GWAS的一项重要工作,旨在GWAS结果的基础上鉴定与表型相关的eQTL和mQTL位点。 传统的GWAS是将全基因组范围内的常见变异进行关联分析,鉴定与表型相关的基因座,但鉴定出来的位点大多数位于基因间隔区,其如何通过基因或者通路影响表型很难被阐述。
--group-analysis level1class \ --flag-filter-data True \ --flag-raw-count True SCZ在不同细胞的表达水平差异: # scDRS group-level statistics for SCZ!catsingle_cell_data/cwy/SCZ.scdrs_group.level1class | column -t -s $'\t'
蓝色和绿色基因均是通过TWAS鉴定出来的与GWAS相关的基因 灰色点表示原始的 GWAS P 值 蓝色点表示校正了绿色基因后的 GWAS P 值 如图所示,经校正后。灰色的点变成了蓝色点(显著变为不显著),说明绿色基因影响了GWAS表型。 http://gusevlab.org/projects/fusion/...
Abstract 1102: Post Gwas Functional Genomics Analysis To Identify Non-coding Single Nucleotide Polymorphisms Controlling The Risk Of Spontaneous Coronary Artery Dissection doi:10.1161/atvb.44.suppl_1.1102Coronary artery diseaseDissectionGenome-wide association studies (GWAS)Background:Spontaneous Coronary Artery...
Enrichment Analysis Based on Snp Heritability 基于Snp遗传力的富集分析 遗传力是由于遗传变异导致的性状变异的比例。SNP遗传力是由一组给定的SNP解释的表型变异量。已经开发了许多方法来估计性状的SNP遗传力,使用个体水平的基因型或来自GWAS的汇总统计 LDSC(Finucane等人,2015):如果GWAS变体在功能类别中富集,那么属于...
Annotation of GWAS peaks The sizes of the confidence intervals (CI) of QTL ranged from 1 bp to 3.3 Mbp; each CI contained between 1 and 1004 variants with significant effects (99.3 on average). While only ca. 6% of the tested variants were included on SNP chips, these chip variants (ma...